Pattern Matching on Weighted Sequences

Weighted sequences are used extensively as profiles for protein families, in the representation of binding sites and often for the representation of sequences produced by a shotgun sequencing strategy. We present various fundamental pattern matching problems on weighted sequences and their respective algorithms. In addition, we define two matching probabilistic measures and we give algorithms for each of these measures. The uncertainty introduced in weighed sequences can also be used as a means to perform approximate string matching. To the best of our knowledge, this is the first time these problems are tackled in this setting.